Uses of Interface
org.biojava.bio.symbol.FiniteAlphabet

Packages that use FiniteAlphabet

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.automata
org.biojava.utils.regex	This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ga.util	Utility functions and helper classes

Uses of FiniteAlphabet in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	SubstitutionMatrix.getAlphabet() Gives the alphabet used by this matrix.

Methods in org.biojava.bio.alignment with parameters of type FiniteAlphabet

Modifier and Type	Method and Description
static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader) Return a new substitution matrix with the specified alphabet.
static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader, String name) Return a new substitution matrix with the specified alphabet and name.

Constructors in org.biojava.bio.alignment with parameters of type FiniteAlphabet

Constructor and Description
SubstitutionMatrix(FiniteAlphabet alpha, File matrixFile) This constructs a SubstitutionMatrix object that contains two Map data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.
SubstitutionMatrix(FiniteAlphabet alpha, short match, short replace) Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.
SubstitutionMatrix(FiniteAlphabet alpha, String matrixString, String name) With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

Uses of FiniteAlphabet in org.biojava.bio.dist

Constructors in org.biojava.bio.dist with parameters of type FiniteAlphabet

Constructor and Description
IndexedCount(FiniteAlphabet fa) Get a new IdexedCount for an alphabet using the default indexer.
SimpleDistribution(FiniteAlphabet alphabet) make an instance of SimpleDistribution for the specified Alphabet.
UniformDistribution(FiniteAlphabet alphabet) Create a new UniformDistribution.
UntrainableDistribution(FiniteAlphabet alpha) Construct a new untrainable distribution over the specified alphabet.

Uses of FiniteAlphabet in org.biojava.bio.dp

Methods in org.biojava.bio.dp that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	WMAsMM.stateAlphabet()
FiniteAlphabet	SimpleMarkovModel.stateAlphabet()
FiniteAlphabet	MarkovModel.stateAlphabet() FiniteAlphabet of the states.
FiniteAlphabet	WMAsMM.transitionsFrom(State from)
FiniteAlphabet	SimpleMarkovModel.transitionsFrom(State from)
FiniteAlphabet	MarkovModel.transitionsFrom(State source) Returns the FiniteAlphabet of all states that have a transition from 'source'.
FiniteAlphabet	WMAsMM.transitionsTo(State to)
FiniteAlphabet	SimpleMarkovModel.transitionsTo(State to)
FiniteAlphabet	MarkovModel.transitionsTo(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.

Uses of FiniteAlphabet in org.biojava.bio.gui

Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet

Constructor and Description
SimpleSymbolStyle(FiniteAlphabet alphabet)

Uses of FiniteAlphabet in org.biojava.bio.program.abi

Fields in org.biojava.bio.program.abi declared as FiniteAlphabet

Modifier and Type	Field and Description
static FiniteAlphabet	ABITools.QUALITY The quality alphabet.

Uses of FiniteAlphabet in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred that return FiniteAlphabet

Modifier and Type	Method and Description
static FiniteAlphabet	PhredTools.getPhredAlphabet() Retrieves the PHRED alphabet from the AlphabetManager.

Uses of FiniteAlphabet in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	DataStore.getAlphabet() The alphabet of symbol lists that can be searched against this DataStore.
FiniteAlphabet	CompactedDataStore.getAlphabet()

Uses of FiniteAlphabet in org.biojava.bio.program.ssbind

Methods in org.biojava.bio.program.ssbind that return FiniteAlphabet

Modifier and Type	Method and Description
static FiniteAlphabet	AlphabetResolver.resolveAlphabet(String identifier) resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier.

Uses of FiniteAlphabet in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff with parameters of type FiniteAlphabet

Modifier and Type	Method and Description
static Sequence	XFFTools.readXFF(File xffFile, String seqID, FiniteAlphabet alpha)

Uses of FiniteAlphabet in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	StructureTools.getStructure()

Uses of FiniteAlphabet in org.biojava.bio.search

Constructors in org.biojava.bio.search with parameters of type FiniteAlphabet

Constructor and Description
SeqContentPattern(FiniteAlphabet alpha) Create a new SeqContentPattern over an alphabet.

Uses of FiniteAlphabet in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return FiniteAlphabet

Modifier and Type	Method and Description
static FiniteAlphabet	ProteinTools.getAlphabet() Gets the protein alphabet
static FiniteAlphabet	RNATools.getCodonAlphabet() Gets the (RNA x RNA x RNA) Alphabet
static FiniteAlphabet	DNATools.getCodonAlphabet() Gets the (DNA x DNA x DNA) Alphabet
static FiniteAlphabet	DNATools.getDNA() Return the DNA alphabet.
static FiniteAlphabet	DNATools.getDNAxDNA() Gets the (DNA x DNA) Alphabet
static FiniteAlphabet	NucleotideTools.getNucleotide() Return the Nucleotide alphabet.
static FiniteAlphabet	RNATools.getRNA() Return the RNA alphabet.
static FiniteAlphabet	ProteinTools.getTAlphabet() Gets the protein alphabet including the translation termination symbols

Uses of FiniteAlphabet in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return FiniteAlphabet

Modifier and Type	Method and Description
static FiniteAlphabet	SeqIOTools.getAlphabet(int identifier) Deprecated. getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.

Constructors in org.biojava.bio.seq.io with parameters of type FiniteAlphabet

Constructor and Description
NameTokenization(FiniteAlphabet fab) Construct a new NameTokenization, defaulting to case-insensitive.
NameTokenization(FiniteAlphabet fab, boolean caseSensitive)

Uses of FiniteAlphabet in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement FiniteAlphabet

Modifier and Type	Class and Description
class	AbstractAlphabet An abstract implementation of Alphabet.
static class	IntegerAlphabet.SubIntegerAlphabet A class to represent a finite contiguous subset of the infinite IntegerAlphabet
class	SimpleAlphabet A simple no-frills implementation of the FiniteAlphabet interface.
class	SingletonAlphabet An alphabet that contains a single atomic symbol.
class	SoftMaskedAlphabet Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.

Fields in org.biojava.bio.symbol declared as FiniteAlphabet

Modifier and Type	Field and Description
static FiniteAlphabet	Alphabet.EMPTY_ALPHABET A really useful static alphabet that is always empty.

Methods in org.biojava.bio.symbol that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	SuffixTree.getAlphabet() Return the Alphabet containing all Symbols which might be found in this SuffixTree.
FiniteAlphabet	Packing.getAlphabet() The FiniteAlphabet this packing is for.
FiniteAlphabet	DNANoAmbPack.getAlphabet()
FiniteAlphabet	DNAAmbPack.getAlphabet()
FiniteAlphabet	AlphabetIndex.getAlphabet() Retrieve the alphabet that this indexes.
protected FiniteAlphabet	SoftMaskedAlphabet.getDelegate() The compound alpha that holds the symbols used by this wrapper
static FiniteAlphabet	CodonPrefTools.getDinucleotideAlphabet() returns an RNA dinucleotide alphabet.
FiniteAlphabet	SoftMaskedAlphabet.getMaskedAlphabet() Gets the Alphabet upon which masking is being applied

Methods in org.biojava.bio.symbol with parameters of type FiniteAlphabet

Modifier and Type	Method and Description
static Symbol	AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha) Return the ambiguity symbol which matches all symbols in a given alphabet.
static Set	AlphabetManager.getAllSymbols(FiniteAlphabet alpha) Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
static AlphabetIndex	AlphabetManager.getAlphabetIndex(FiniteAlphabet alpha) Get an indexer for a specified alphabet.
static SoftMaskedAlphabet	SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask) Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
static SoftMaskedAlphabet	SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask, SoftMaskedAlphabet.MaskingDetector maskingDetector) Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
static Packing	PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity) Get the default packing for an alphabet.

Constructors in org.biojava.bio.symbol with parameters of type FiniteAlphabet

Constructor and Description
DummySymbolList(FiniteAlphabet alpha, int length)
SimpleGeneticCodeTable(FiniteAlphabet source, FiniteAlphabet target) Creates a new instance of SimpleGeneticCodeTable
SimpleManyToOneTranslationTable(FiniteAlphabet source, FiniteAlphabet target) Construct a new translation table.
SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target) Construct a new translation table.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target) Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target, Map transMap) Create a new translation table that will translate symbols from source to target.
SuffixTree(FiniteAlphabet alphabet) Construct a new SuffixTree to contain motifs over the specified alphabet.
UkkonenSuffixTree(FiniteAlphabet alpha)

Uses of FiniteAlphabet in org.biojava.utils.automata

Constructors in org.biojava.utils.automata with parameters of type FiniteAlphabet

Constructor and Description
Nfa(String name, FiniteAlphabet alfa)
PatternBlitz(FiniteAlphabet alfa, org.biojava.utils.automata.StateMachineToolkit factory)

Uses of FiniteAlphabet in org.biojava.utils.regex

Methods in org.biojava.utils.regex that return FiniteAlphabet

Modifier and Type	Method and Description
FiniteAlphabet	Pattern.getAlphabet()

Methods in org.biojava.utils.regex with parameters of type FiniteAlphabet

Modifier and Type	Method and Description
static PatternFactory	PatternFactory.makeFactory(FiniteAlphabet alfa) Returns a factory for Patterns in the specified Alphabet.

Constructors in org.biojava.utils.regex with parameters of type FiniteAlphabet

Constructor and Description
Search(FiniteAlphabet alfa)

Uses of FiniteAlphabet in org.biojavax.bio.seq

Constructors in org.biojavax.bio.seq with parameters of type FiniteAlphabet

Constructor and Description
InfinitelyAmbiguousSymbolList(FiniteAlphabet fa) Creates a new instance of InfinitelyAmbiguousSymbolList

Uses of FiniteAlphabet in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return FiniteAlphabet

Modifier and Type	Method and Description
static FiniteAlphabet	GATools.getBinaryAlphabet() Gets a Reference to the FlyWeight GA_Binary Alphabet.

Methods in org.biojavax.ga.util with parameters of type FiniteAlphabet

Modifier and Type	Method and Description
static OrderNDistribution	GATools.standardMutationDistribution(FiniteAlphabet a) Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0)
static OrderNDistribution	GATools.uniformMutationDistribution(FiniteAlphabet a) Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).